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Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on

Issue 2 • Date Feb. 2006

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  • Table of contents

    Page(s): c1
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  • IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems publication information

    Page(s): c2
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  • Guest Editorial

    Page(s): 209 - 210
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  • Microfluidics-Based Biochips: Technology Issues, Implementation Platforms, and Design-Automation Challenges

    Page(s): 211 - 223
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    Microfluidics-based biochips are soon expected to revolutionize clinical diagnosis, deoxyribonucleic acid (DNA) sequencing, and other laboratory procedures involving molecular biology. In contrast to continuous-flow systems that rely on permanently etched microchannels, micropumps, and microvalves, digital microfluidics offers a scalable system architecture and dynamic reconfigurability; groups of unit cells in a microfluidics array can be reconfigured to change their functionality during the concurrent execution of a set of bioassays. As more bioassays are executed concurrently on a biochip, system integration and design complexity are expected to increase dramatically. This paper presents an overview of an integrated system-level design methodology that attempts to address key issues in the synthesis, testing and reconfiguration of digital microfluidics-based biochips. Different actuation mechanisms for microfluidics-based biochips, and associated design-automation trends and challenges are also discussed. The proposed top-down design-automation approach is expected to relieve biochip users from the burden of manual optimization of bioassays, time-consuming hardware design, and costly testing and maintenance procedures, and it will facilitate the integration of fluidic components with a microelectronic component in next-generation systems-on-chips (SOCs). View full abstract»

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  • Modeling and Simulation of Electrified Droplets and Its Application to Computer-Aided Design of Digital Microfluidics

    Page(s): 224 - 233
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    Digital microfluidics is the second-generation lab-on-a-chip architecture based upon micromanipulation of droplets via a programmed external electric field by an individually addressable electrode array. Dielectrophoresis (DEP) and electrowetting-on-dielectric (EWOD) are of dominant operating principles. The microfluidic mechanics of manipulating electrified droplets are complex and not entirely understood. This paper presents a numerical simulation method based on droplet electrohydrodynamics. First, a systematic validation study is shown comparing the simulation solution with both analytical and experimental data, quantitatively and qualitatively, and in both steady state and transient time sequences. Such comparison exhibits excellent agreement. Simulations are then used to illustrate its application to computer-aided design of both EWOD-driven and DEP-driven digital microfluidics. View full abstract»

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  • Modeling, Simulation, and Optimization of Electrowetting

    Page(s): 234 - 247
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    Electrowetting is an elegant method to realize the motion, dispensing, splitting, and mixing of single droplets in a microfluidic system without the need for any mechanical—and fault-prone—components. By only applying an electric voltage, the interfacial energy of the fluid–solid interface is altered and the contact line of the droplet is changed. However, since the droplet shape is usually heavily distorted, it is difficult to estimate the droplet shape during the process. Further, it is often necessary to know if a process, e.g., droplet splitting on a given geometry, is possible at all, and what can be done to increase the system's reliability. It is thus important to use computer simulations to gain an understanding about the behavior of a droplet for a given electrode geometry and voltage curve. Special care must be exercised when considering surface-tension effects. We present computer simulations done with the Surface Evolver program and a template library combined with a graphical user interface (GUI) that facilitates standard tasks in the simulation of electrowetting arrays. View full abstract»

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  • Algorithms in FastStokes and Its Application to Micromachined Device Simulation

    Page(s): 248 - 257
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    For a wide variety of micromachined devices, designers need accurate analysis of fluid drag forces for complicated three-dimensional (3-D) problems. This paper describes FastStokes, a recently developed 3-D fluid analysis program. FastStokes rapidly computes drag forces on complicated structures by solving an integral formulation of the Stokes equation using a precorrected fast Fourier transform (PFFT)-accelerated boundary element method (BEM). The specializations of the PFFT algorithm to the Stokes flow problem are described, and computational results are presented. Timing results are used to demonstrate that FastStokes scales almost linearly with problem complexity, can easily analyze structures as complicated as an entire comb drive in under an hour, and can produce results that accurately match measured data. View full abstract»

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  • Composable Behavioral Models and Schematic-Based Simulation of Electrokinetic Lab-on-a-Chip Systems

    Page(s): 258 - 273
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    This paper presents composable behavioral models and a schematic-based simulation methodology to enable top-down design of electrokinetic (EK) lab-on-a-chip (LoC). Complex EK LoCs are shown to be decomposable into a system of elements with simple geometry and specific function. Parameterized and analytical models are developed to describe the electric and biofluidic behavior within each element. Electric and biofluidic pins at element terminals support the communication between adjacent elements in a simulation schematic. An analog hardware description language implementation of the models is used to simulate LoC subsystems for micromixing and electrophoretic separation. Both direct current (dc) and transient analysis can be performed to capture the influence of system topology, element sizes, material properties, and operational parameters on LoC system performance. Accuracy (relative error generally less than 5%) and speedup$(≫hbox100times)$of the schematic-based simulation methodology are demonstrated by comparison to experimental measurements and continuum numerical simulation. View full abstract»

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  • FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation

    Page(s): 274 - 284
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    This paper presents a fast boundary-element method (BEM) algorithm that is well suited for solving electrostatics problems that arise in traditional and bio-microelectromechanical systems (bio-MEMS) design. The algorithm, FFTSVD, is Green's-function-independent for low-frequency kernels and efficient for inhomogeneous problems. FFTSVD is a multiscale algorithm that decomposes the problem domain using an octree and uses sampling to calculate low-rank approximations to dominant source distributions and responses. Long-range interactions at each length scale are computed using the FFT. Computational results illustrate that the FFTSVD algorithm performs better than precorrected-FFT (pFFT)-style algorithms or the multipole-style algorithms in FastCap. View full abstract»

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  • Macromodel Generation for BioMEMS Components Using a Stabilized Balanced Truncation Plus Trajectory Piecewise-Linear Approach

    Page(s): 285 - 293
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    In this paper, we present a technique for automatically extracting nonlinear macromodels of biomedical microelectromechanical systems devices from physical simulation. The technique is a modification of the recently developed trajectory piecewise-linear approach, but uses ideas from balanced truncation to produce much lower order and more accurate models. The key result is a perturbation analysis of an instability problem with the reduction algorithm, and a simple modification that makes the algorithm more robust. Results are presented from examples to demonstrate dramatic improvements in reduced model accuracy and show the limitations of the method. View full abstract»

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  • System-Level Simulation of Flow-Induced Dispersion in Lab-on-a-Chip Systems

    Page(s): 294 - 304
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    The development of lab-on-a-chip systems has moved from the demonstration of individual components to a complex assembly of components. Due to the increased complexities associated with model setup and computational time requirements, current design approaches using spatial and time-resolved multiphysics modeling, though viable for component-level characterization, become unaffordable for system-level design. To overcome these limitations, we present models for the system-level simulation of fluid flow, electric field, and analyte dispersion in microfluidic devices. Compact models are used to compute the flow (pressure driven and electroosmotic) and are based on the integral formulation of the mass, momentum, and current conservation equations. An analytical model based on the method-of-moments approach has been developed to characterize the dispersion induced by combined pressure and electrokinetic-driven flow. The methodology has been validated against detailed three-dimensional (3-D) simulations and has been used to analyze hydrostatic-pressure effects in electrophoretic separation chips. A 100-fold improvement in the computational time without significantly compromising the accuracy (error less than 10%) has been demonstrated. View full abstract»

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  • Computer-Aided Optimization of DNA Array Design and Manufacturing

    Page(s): 305 - 320
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    DNA probe arrays, or DNA chips, have emerged as a core genomic technology that enables cost-effective gene expression monitoring, mutation detection, single nucleotide polymorphism analysis, and other genomic analyses. DNA chips are manufactured through a highly scalable process called very large-scale immobilized polymer synthesis (VLSIPS) that combines photolithographic technologies adapted from the semiconductor industry with combinatorial chemistry. Commercially available DNA chips contain more than half a million probes and are expected to exceed 100 million probes in the next generation. This paper is one of the first attempts to apply very large scale integration (VLSI) computer-aided design methods to the physical design of DNA chips, where the main objective is to minimize total border cost (i.e., the number of nucleotide mismatches between adjacent sites). By exploiting analogies between manufacturing processes for DNA arrays and for VLSI chips, the authors demonstrate the potential for transfer of methodologies from the 40-year-old field of electronic design automation to the newer DNA array design field. The main contributions of this paper are the following. First, it proposes several partitioning-based algorithms for DNA probe placement that improve solution quality by over 4% compared to best previously known methods. Second, it gives a new design flow for DNA arrays, which enhances current methodologies by adding flow awareness to each optimization step and introducing feedback loops. Third, it proposes solution methods for new formulations integrating multiple design steps, including probe selection, placement, and embedding. Finally, it introduces new techniques to experimentally evaluate the scalability and suboptimality of existing and newly proposed probe placement algorithms. Interestingly, the authors find that DNA placement algorithms appear to have better suboptimality properties than those recently reported for VLSI placement algorithms [C.- C. Chang et al., Optimality and scalability study of existing placement algorithms, Proc. Asia South-Pacific Design Automation Conf., Kitakyushu, Japan, p.621-7, Jan. 2003; J. Cong et al., Optimality, scalability and stability study of partitioning and placement algorithms, Proc. Int. Symp. Physical Design (ISPD), Monterey, CA, p.88-94, 2003] View full abstract»

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  • Synthesis of Multiplexed Biofluidic Microchips

    Page(s): 321 - 333
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    Lab-on-a-chip (LoC) devices are a class of microfluidic chip-based systems that show a great deal of promise for complex chemical and biological sensing and analysis applications. An approach for full-custom LoC design, which leverages optimal design techniques and system-on-a-chip (SoC) physical design methods, is being developed. Both physical design of the chip and microfluidic performance are simultaneously considered to obtain complete LoC layouts. The proposed approach is demonstrated by designing multiplexed capillary electrophoresis (CE) separation microchips. The authors believe that this approach provides a foundation for future extension to LoC devices in which many different complex chemical operations are performed entirely on-chip. View full abstract»

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  • Modeling and Controlling Parallel Tasks in Droplet-Based Microfluidic Systems

    Page(s): 334 - 344
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    This paper presents general hardware-independent models and algorithms to automate the operation of droplet-based microfluidic systems. In these systems, discrete liquid volumes of typically less than 1$muhboxl$are transported across a planar array by dielectrophoretic or electrowetting effects for biochemical analysis. Unlike in systems based on continuous flow through channels, valves, and pumps, the droplet paths can be reconfigured on demand and even in real time. Algorithms that generate efficient sequences of control signals for moving one or many droplets from start to goal positions, subject to constraints such as specific features and obstacles on the array surface or limitations in the control circuitry, are developed. In addition, an approach toward automatic mapping of a biochemical analysis task onto a DMFS is investigated. Achieving optimality in these algorithms can be prohibitive for large-scale configurations because of the high asymptotic complexity of coordinating multiple moving droplets. Instead, these algorithms achieve a compromise between high runtime efficiency and a more limited nonglobal optimality in the generated control sequences. View full abstract»

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  • Performance Characterization of a Reconfigurable Planar-Array Digital Microfluidic System

    Page(s): 345 - 357
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    This paper describes a computational approach to designing a digital microfluidic system (DMFS) that can be rapidly reconfigured for new biochemical analyses. Such a “lab-on-a-chip” system for biochemical analysis, based on electrowetting or dielectrophoresis, must coordinate the motions of discrete droplets or biological cells using a planar array of electrodes. The authors have earlier introduced a layout-based system and demonstrated its flexibility through simulation, including the system's ability to perform multiple assays simultaneously. Since array-layout design and droplet-routing strategies are closely related in such a DMFS, their goal is to provide designers with algorithms that enable rapid simulation and control of these DMFS devices. In this paper, the effects of variations in the basic array-layout design, droplet-routing control algorithms, and droplet spacing on system performance are characterized. DMFS arrays with hardware limited row-column addressing are considered, and a polynomial-time algorithm for coordinating droplet movement under such hardware limitations is developed. To demonstrate the capabilities of our system, we describe example scenarios, including dilution control and minimalist layouts, in which our system can be successfully applied. View full abstract»

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  • A Pattern-Mining Method for High-Throughput Lab-on-a-Chip Data Analysis

    Page(s): 358 - 377
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    Biochips are emerging as a useful tool for high-throughput acquisition of biological data and continue to grow in information quality and in discovering new applications. Recent advances include CMOS-based integrated biosensor arrays for deoxyribonucleic acid (DNA) expression analysis (Hassibi and Lee, 2005), (Schienle , 2004), and active research is ongoing for the miniaturization and integration of protein microarrays (Kiyonaka , 2004), (Rubina , 2003), (Scrivener , 2003), tissue microarrays (TMAs), (Chen , 2004), (Shergill , 2004), and fluorescence-based multiplexed cytokine immunoassays (Wang , 2002). The main advantages of microfluidic lab-on-a-chip include ease of use, speed of analysis, low sample and reagent consumption, and high reproducibility due to standardization and automation. Without effective data-analysis methods, however, the merit of acquiring massive data through biochips will be marginal. The high-dimensional nature of such data requires novel techniques that can cope with the curse of dimensionality better than conventional data-analysis approaches. In this paper, the authors proposed a pattern-mining method to analyze large-scale biological data obtained from high-throughput biochip experiments. In particular, when a data set is given as a matrix, the method can find patterns appearing in the form of (possibly overlapping) submatrices of the input matrix. The method exploits the techniques developed for the symbolic manipulation of Boolean functions. Leveraged by this approach, the method can find, given a data matrix, all patterns that satisfy specific input parameters. The authors tested the method with several large-scale biochip data and observed that the proposed method outperforms the alternatives in terms of efficiency and the number of patterns discovered. View full abstract»

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  • Microfluidic Injector Models Based on Artificial Neural Networks

    Page(s): 378 - 385
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    Lab-on-a-chip (LoC) systems can be functionally decomposed into their basic operating devices. Common devices are mixers, reactors, injectors, and separators. In this paper, the injector device is modeled using artificial neural networks (NNs) trained with finite element simulations of the underlying mass transport partial differential equations (PDEs). This technique is used to map the injector behavior into a set of analytical performance functions parameterized by the system's physical variables. The injector examples shown are the cross, the double-tee, and the gated-cross. The results are four orders of magnitude faster than numerical simulation and accurate with mean square errors (MSEs) on the order of$10^-4$. The resulting NN training data compare favorably with experimental data from a gated-cross injector found in the literature. View full abstract»

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  • 49th IEEE International Midwest Symposium on Circuits and Systems (MWSCAS 2006)

    Page(s): 386
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  • International Symposium on Low Power Electronics and Design (ISLPED'06)

    Page(s): 387
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  • 2006 IEEE International Symposium on Circuits and Systems (ISCAS 2006)

    Page(s): 388
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  • IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems society information

    Page(s): c3
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  • IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems Information for authors

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Aims & Scope

The purpose of this Transactions is to publish papers of interest to individuals in the areas of computer-aided design of integrated circuits and systems.

Full Aims & Scope

Meet Our Editors

Editor-in-Chief

VIJAYKRISHNAN NARAYANAN
Pennsylvania State University
Dept. of Computer Science. and Engineering
354D IST Building
University Park, PA 16802, USA
vijay@cse.psu.edu